I managed to partially solve this issue. Notwithstanding the fact I still can't get anything but a blank picture, when I playback the video via justin.tv's player, after examining the .flv file itself (downloaded it from justin.tv by the direct link), it can be played via a mediaplayer, such as Totem Movie Player.

Hence there has to be some major difference between formats of custom .flv videos, which might be easily played via justin.tv player and those, which are recorded during the screencasting and give a dark screen on justin.tv. Audio is fine regardless.